The design matrix does not match the FSGD file. It could be because you have commas (i,e ",") instead of decimal points (ie, ".") in the FSGD file. Try replacing and rerunning.
On 03/08/2017 04:32 AM, teodora petrova wrote: > Hello, > > I am trying to test for the effect of different variables on cortical > thickness. The variables (with type) are: index (continuous). > Gender(factor), Age(continuous), Years of education (continuous), > Depression (factor), Vascular comorbidity (factor), and MMSE > (continuous). Later, I need to correlate thickness with my variable of > interest (index). Depending on the results of the current analysis, I > will choose which of the other variables will be my covariates. > > Here is what I attempted to do so far and the error I got: > > I have constructed the fsgd file according to the example with one > group and covariates (see attahced to this email). My contrasts look > like, for example: 0 1 0 0 0 0 0 (to test effects of gender), and 0 0 > 1 0 0 0 0 (to test for the effects of age). > I am following the commands in the Group Analysis tutorial. I pass > successfully mris_preproc and mri_surf2surf. > When I get to mri_glmfit, I receive the error: > > ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 > > Possible problem with experimental design: > Check for duplicate entries and/or lack of range of > continuous variables within a class. > > 1. My command line is > mri_glmfit --y lh.newindex.thickness.10.mgh --fsgd FSGD.fsgd dods --C > index.mtx --C gender.mtx --C age.mtx --C education.mtx --C depression.mtx --C > vascularc.mtx --C MMSE.mtx --surf fsaverage lh --cortex --glmdir > lh.newindex.glmdir > 2. Please find attachced my fsgd file > 3. Find attached the Design matrix > > What is the best way to construct the fsgd and contrasts? > In the version I am sending, I have demeaned all continuous variables. > Is that something you will recommend to do? (I tried the group > analysis with a fsgd file containing the normal, non-demeaned values, > but got the same error). > > Thank you for the help! > > Best, > Teodora > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
